#PBS -N multiqc
#PBS -A GT-wratcliff3
#PBS -q inferno
#PBS -l nodes=1:ppn=6
#PBS -l pmem=4gb
#PBS -l walltime=1:00:00
#PBS -j oe
#PBS -m abe
#PBS -M ktong34@gatech.edu
    
# change to project directory
PROJECT_DIR=$PBS_O_WORKDIR
echo "Changing directory to ${PROJECT_DIR}…"
cd $PROJECT_DIR
     
# activate environment
PIPELINE_ENV=`basename scripts/*.yml .yml`
echo "Activating conda environment ${PIPELINE_ENV}…"
source activate $PIPELINE_ENV

# main
mkdir $1
multiqc \
. \
-o $1 \
-n `basename $1`_report \
-f

